Searching the Porphyromonas gingivalis genome with peptide fragmentation mass spectra

An approach is described for genomic database searching based on experiment ally observed proteolytic fragments, e.g., isolated from 1D or 2D gels or a nalyzed directly, that can be applied to unfinished prokaryotic genomic dat a in the absence of annotations or previously assigned open reading frames (ORFs). This variation on the database search is in contrast to the more fa miliar use of peptide mass spectral fragmentation data to search fully anno tated inferred protein databases, e.g., OWL or SWISS-PROT. We compared the SEQUEST search results from a six reading frame translation of the Porphyro monas gingivalis genome DNA sequence with those from computationally derive d ORFs created using publicly available genomics software tools. The ORF ap proach eliminated many of the artifacts present in output from the six read ing frame search. The method was applied to uninterpreted tandem mass spect rometric data derived from proteins secreted by the periodontal pathogen Po rphyromonas gingivalis in response to the gingival epithelial cell environm ent, a model system for the study of host-pathogen interactions relevant to human periodontal disease.